A forum for discussing matters of moment, from a curmudgeonly perspective. (The ideas posted here do not necessarily represent those of any organization with which I am a part). Rude and insulting remarks will not be published, but civil disagreement is welcome.

Friday, November 03, 2006

Dr. Jonathan Wells Responds to Critics

[The following comments are from Jonathan Wells in light of the controversy raging on this blog. Thanks to Dr. Wells for providing this essay exclusively for The Constructive Curmudgeon.]

Comment for Doug Groothuis’s blog:

The issue here is not all that complicated. Darwin thought that “community in embryonic structure reveals community of descent” and concluded that early vertebrate embryos “show us, more or less completely, the condition of the progenitor of the whole group in its adult state.” Darwin considered this “by far the strongest single class of facts in favor of” his theory. (Origin of Species, Chapter XIV; September 10, 1860 letter to Asa Gray)

But early vertebrate embryos do not look alike. They become somewhat similar (though not as similar as Haeckel made them out to be) midway through development, then they diverge again. This is illustrated by the “developmental hourglass” drawing on page 31 of my Politically Incorrect Guide to Darwinism and Intelligent Design. Developmental biologists (including P.Z. Myers, to judge from his Panda’s Thumb review of my chapter) are well aware of this pattern, which has been described repeatedly in the developmental biology literature.

But an hourglass pattern does not provide the evidence Darwin needed for his theory. If “community in embryonic structure reveals community of descent,” then a pattern of early differences followed by convergence followed by divergence makes no sense. Some modern Darwinists, instead of acknowledging the problem, simply attribute the early differences to evolution. In other words, they assume their theory is true and then use it to explain away anomalies in the very evidence that was supposed to provide the strongest support for it. Meanwhile, other Darwinists provide a smokescreen for this circular argument by calling their critics names…

37 comments:

In other words, they assume their theory is true and then use it to explain away anomalies in the very evidence that was supposed to provide the strongest support for it. Meanwhile, other Darwinists provide a smokescreen for this circular argument by calling their critics names…

You know - I'm ultimately not sure where I stand on ID. And I don't have the expertise to judge Wells' arguments or those of Myers. I will say that some of the people coming over from Myers' blog and commenting disgust me. If folks like this think that all of that hatred, anger, and venom (so often evident in Myers as well) is supposed to somehow be mustered up into some forceful intellectual case against ID, they are seriously deluding themselves. Perhaps that gives them some sort of political momentum - serving as a rallying cry for people of like sensibilities. But when I'm trying to look at an issue objectively, that kind of behavior and rhetoric on the part of a proponent is the *first* indicator of an inability to restrain bias. These are the kinds of people I steer clear of.

Another one of my first principles is to never accuse an academic of lying without *extremely* strong evidence that this is the case, and I am extremely skeptical of the agenda of those who do this. Why? Well, its just initially very improbable that academics would blatantly lie about an issue in some sort of conscious manner. It is much too big of a risk, given how much stake they have in the public perception of their credibility. This is also why there is so much more of a need for caution on the part of the accuser. You can do alot of harm to the accused if you're wrong. This isn't politics where everyone expects the opponents to call each other liars (if not actually *be* liars!). It is so much more likely that academics are simply mistaken in these instances, or allowing their biases to skew the truth, than that they are knowingly telling a lie. Whenever I see someone calling another academic a "liar", especially on flimsy evidence, it is *that* person who loses credibility in my eyes. In almost every instance I've seen it is a hasty judgement made on too little evidence, usually done for the purpose of character assassination.

Now - McGrew made the mistake of playing Myers' game. I saw that from his initial response and thought it was regretful. But he retracted it, and in that, he's exemplary. It is very rare to see someone who has accused another academic of lying apologize. This requires a good deal of humility, because there's a moral component to the initial accusation. They were wrong, not just factually, but morally, in jumping the gun and tarnishing a fellow academic's reputation. I predict that we will not see such an apology or concession from Myers for this very reason.

McGrew's overall tone in pretty much all of the comments he's written (with the exception of his hasty accusation of dishonesty towards Myers) is exemplary, and his writing is well-reasoned and level-headed. I feel the same way about Wells response here. Myers, OTOH, strikes me as just the opposite in nearly everything he writes on his blog.

Yes, the venom is off-putting. I find the venom in Dr. Wells' arguments equally off-putting, even when he delivers them smiling and without profanity.

Ryan, is an untruthful statement made something closer to the truth when it is delivered politely?

Dr. Wells' claim about Dr. Ballard's views is false. It is the type of claim made in other works by wells, and I would commend to you the footnotes in the chapter on peppered moths in Wells' book, Icons of Evolution. I urge you to look at that chapter, and check it out like this: List the scientists he cites as authorities, and look up their comments on Wells' treatment of their works -- or write them, as I did. Without exception, the living ones have repudiated Dr. Wells' claims about their work.

Without exception.

Even after Judith Hooper described how creationists could distort her work simply describing the research, falsely, to make it appear as if the moth experiments were in error, Wells did exactly that in his presentation to the Texas State Board of Education, footnoting her as if she supported his claims instead of opposed them. Does chutzpah lend veracity? It should not.

At what point do we ask an author to correct such claims, made by cutting and pasting snippets of sentences into claims that the original authors did not make? I believe ethical people should do that now.

And so I ask Dr. Wells to correct his claims, here and now, and repent from such work in the future.

Dini changed no facts. Dini told no lies. Dini asked only that kid asking for recommendations to medical school be able to demonstrate they had mastered the material in his classes, and that they take the classes and get good grades.

In the end, the Justice Department, after a classic Ashcroft Inquisition-style move, agreed there was no problem.

Or were you referring to Phillip Johnson? I don't believe he and I see eye to eye on much. His fast-and-loose methods with the facts make me worry about whether he ever actually taught evidence at Berkeley.

Jonathan Wells wrote:"If “community in embryonic structure reveals community of descent,” then a pattern of early differences followed by convergence followed by divergence makes no sense."

Sure it does. One only needs to understand morphogenesis and the ability of blastulas to regulate.

This is why you avoid explaining the fact that cells can be removed or added (by microinjection) to blastulae without killing or deforming the resulting embryo and adult. We do it all the time. Since these stages are so plastic, there's no great morphological constraint. When complexity increases by the pharyngula stage, there are significant morphological constraints.

This is all experimental evidence, which you omit to deceive your audience in favor of quote-mining a review from a dead guy.

"Some modern Darwinists, instead of acknowledging the problem, simply attribute the early differences to evolution."

Since I just attributed the early differences to morphological plasticity, your hand-waving is meaningless.

"In other words, they assume their theory is true and then use it to explain away anomalies in the very evidence that was supposed to provide the strongest support for it."

As I noted above, morphological plasticity (demonstrated experimentally) explains the lack of constraint. The strongest support comes from sequence evidence, which you'll never attempt to explain in its entirety by ID.

"Meanwhile, other Darwinists provide a smokescreen for this circular argument by calling their critics names…"

I won't call you names. I'll just point out that quote-mining reviews by dead men, instead of citing and discussing the actual evidence, is patently dishonest. It's especially cowardly because you clearly lack the faith to test your hypotheses for yourself. Your ASCB poster was a howlingly funny demonstration of that cowardice.

"Is that how science should be done?"

Science should be done by employing hypotheses to predict the results of new observations and experiments, not your cowardly, pseudoscientific quote-mining of someone who is dead and unable to respond.

You've abandoned the production of new evidence (which you weren't exactly successful doing with noncontroversial subjects), because you have no faith in your hypotheses. Why didn't you apply for one of those Templeton Foundation grants?

Well, perhaps Dr.Wells, it should be done like you did it in 'Icons...' - simply lop off the first part of a sentence, quote the rest and make it appear as if it means something it doesn't (re: the Jain, Lake and Rivera butchery you engaged in).

The Ballard incident is just one in a long line of such dishonest antics that Wells and his fellow Christian IDcreationists engage in on a regular basis. It is a shame that their acolytes refuse to see this.

In addition, I also find the 'venom' comments silly. This is a common theme in IDcreationism - those mean, bad evil atheistic evilutionists say such mean things, it must be because they are evil, wrong, desperate, etc., but OUR guys - like Jon Wells and Bill Dembski - the false things they say and the false accusations they hurl are so polite and witty, why, they are such great men...

Thanks for the thoughtful post. Obviously I jumped the gun initially when I thought Myers had fabricated the quotation. I have no problem saying I was wrong there.

If you sift through the comments on the previous thread, you'll see something interesting. There's a claim -- I've asked PZ whether it's true, but I haven't seen an answer yet -- that the original page reference to the quotation in Myers's review on PT was to pp. 30-31 even though the wording was from the call-out box on p. 35 and that Myers, acknowledging the difference, changed the page numbers in the review. But he didn't change the claim that Wells had deceptively left out the reference to the gastrula stage.

When PZ first pointed out the quotation in the call-out box, I concluded that he had simply failed to look at the sentence from which the call-out was condensed. I can understand how that could happen; it's careless, but it's not dishonest. But if this claim is true -- and there is documentation backing it up that suggests that it is -- then the "innocent mistake" position becomes a lot more difficult to maintain.

I'm hoping that PZ will explain what happened there.

The funny thing is, the condensed quotation in the call-out isn't false; it's just vague. The vagueness is cleared up by the actual wording of Wells's text on pp. 30-31. Repeated rants about how Wells has "used similar language before" are not to the point: he's quite explicit here that Ballard is referring to gastrulation and cleavage, and Ballard is referring to these stages -- to the top of the developmental hourglass. So Myers's claim that Wells is trying to pretend that Ballard's statement applies to the pharyngula stage is just wrong.

Would Ballard have endorsed Wells's conclusions? I daresay he would not. But it is possible sometimes make a reasonable case by taking acknowledgments of individual facts from experts and arguing from them to a conclusion that each of those experts would reject. The fact that they would reject the conclusion does not by itself undermine the force of the argument. It does mean that the would-be innovator bears the burden of explaining why, if the facts really do point to X, few or none of the experts on whose work he is relying are willing to draw the conclusion that X. But as long as the facts are used responsibly -- and of course that's what most of the excitement here is all about -- there is nothing a priori illegitimate about making such a case.

"Would Ballard have endorsed Wells's conclusions? I daresay he would not. But it is possible sometimes make a reasonable case by taking acknowledgments of individual facts from experts and arguing from them to a conclusion that each of those experts would reject. The fact that they would reject the conclusion does not by itself undermine the force of the argument. It does mean that the would-be innovator bears the burden of explaining why, if the facts really do point to X, few or none of the experts on whose work he is relying are willing to draw the conclusion that X. But as long as the facts are used responsibly -- and of course that's what most of the excitement here is all about -- there is nothing a priori illegitimate about making such a case."

I agree entirely, Tim.This is what the Darwinists dismiss as "quote mining." But there is nothing logically or ethically flawed about it. I often use a Richard Lewontin quote from The New York Times (reviewing a book by Carl Sagan) in which he says that any materialistic explanation trumps any and every nonmaterialist explanation in science (no matter how bizarre the materialist explanation must seem), because we must presuppose materialism in science. Othewise, it is a "divine foot in the door."

Lewontin is pleased as punch about that, but I take it to beg the question. It also sets up a false dilemma: materialism or "God help us: we've let loose globlins, fairies, ghosts, demons, angels, demigods, and all manner of spooks into the universe such that science will be destroyed and we all will go hurling at full speed back to the Dark Ages."

Is that "quote mining"? No. I take this claim to illustrate an a priori commitment to materialism. Then I attack that commitment.

Tim wrote:"The vagueness is cleared up by the actual wording of Wells's text on pp. 30-31."

No, it isn't.

"Repeated rants about how Wells has "used similar language before" are not to the point: he's quite explicit here that Ballard is referring to gastrulation and cleavage,"

But Ballard points out that the pharyngula is dramatically different, and Wells omits that--because his goal is to deceive his audience.

"... and Ballard is referring to these stages ..."

And to their differences from the pharyngula, which Wells (and you) dishonestly omits.

"Would Ballard have endorsed Wells's conclusions? I daresay he would not."

And Wells's omission of that was dishonest.

"But it is possible sometimes make a reasonable case by taking acknowledgments of individual facts from experts and arguing from them to a conclusion that each of those experts would reject."

This is not one of those times.

"The fact that they would reject the conclusion does not by itself undermine the force of the argument."

No, Wells's use of quote-mining instead of citing evidence undermines his argument. It shows that he has to resort to deception.

"It does mean that the would-be innovator bears the burden of explaining why, if the facts really do point to X, few or none of the experts on whose work he is relying are willing to draw the conclusion that X."

Which quote-mining can't begin to bear.

"But as long as the facts are used responsibly -- and of course that's what most of the excitement here is all about -- there is nothing a priori illegitimate about making such a case."

But the facts are the data, not partial quotes from a review, Tim.

When real scientists disagree with each other, they note the disagreement up front (which Wells failed to do), they cite ALL the relevant data (which Wells failed to do), they make an argument not from quotes but from the data (which Wells failed to do), and they don't bother with quoting the person who they believe is wrong (which Wells did in a most deceptive way).

The other dishonest thing about your approach to supporting Wells, Tim, is that you haven't cited any actual data.

And you still haven't apologized to all the PT commenters whom you falsely accused of intellectual negligence.

If you sift through the comments on the previous thread, you'll see something interesting. There's a claim -- I've asked PZ whether it's true, but I haven't seen an answer yet -- that the original page reference to the quotation in Myers's review on PT was to pp. 30-31 even though the wording was from the call-out box on p. 35 and that Myers, acknowledging the difference, changed the page numbers in the review. But he didn't change the claim that Wells had deceptively left out the reference to the gastrula stage.

Ryan: This is very interesting and worth pursuing. Hopefully, PZ is reading this or someone is relaying it to him.

Tim: The funny thing is, the condensed quotation in the call-out isn't false; it's just vague. The vagueness is cleared up by the actual wording of Wells's text on pp. 30-31. Repeated rants about how Wells has "used similar language before" are not to the point: he's quite explicit here that Ballard is referring to gastrulation and cleavage, and Ballard is referring to these stages -- to the top of the developmental hourglass. So Myers's claim that Wells is trying to pretend that Ballard's statement applies to the pharyngula stage is just wrong.

Ryan: I agree. Very good points...

Tim: Would Ballard have endorsed Wells's conclusions? I daresay he would not. But it is possible sometimes make a reasonable case by taking acknowledgments of individual facts from experts and arguing from them to a conclusion that each of those experts would reject. The fact that they would reject the conclusion does not by itself undermine the force of the argument. It does mean that the would-be innovator bears the burden of explaining why, if the facts really do point to X, few or none of the experts on whose work he is relying are willing to draw the conclusion that X. But as long as the facts are used responsibly -- and of course that's what most of the excitement here is all about -- there is nothing a priori illegitimate about making such a case.

Ryan: I consider this to be one of those matters that should be so obvious to all members of the debate, that it need not even be said. When/if scientists start arguing like this, philosophers need to enter the conversation and give them a good spanking. The dilemma for me is this. If you have to actually explain something as obvious as this to the people you are arguing with, the odds are that their ability to reason is so underdeveloped (or overshadowed) that your line of reasoning here isn't going to sink in. But then again, if you ignore it, this kind of sloppy thinking continues to spread like fire amongst others. I have seen plenty of secular non-scientific blogs, who are fans of Myers and those like him, repeating the often baseless "quote mining" charge to discredit IDers on just these grounds ("Look - the author they quote ultimately disagrees with them! Liars!!!"). So you wind up in a situation where you're stretched so thin, having to waste your time putting out all of these fires. You have to chase down every irrational quote-mining charge, every alleged claim of dishonesty or misrepresentation of the evidence, etc. Meanwhile the Myers fan club begins to swarm on your analysis and multiply irrational inferences like Gremlins at a pool party.

Honestly, I hate politics. That's one of the main reasons I despair of the ID vs. Darwinism debate. It is, on both sides, so often more about politics than reasoning. I guess this is the fate of pretty much every important argument, once its ramifications are seen by the wider public.

Dr. Groothuis said: I often use a Richard Lewontin quote from The New York Times (reviewing a book by Carl Sagan) in which he says that any materialistic explanation trumps any and every nonmaterialist explanation in science (no matter how bizarre the materialist explanation must seem), because we must presuppose materialism in science. Otherwise, it is a "divine foot in the door."

Lewontin is pleased as punch about that, but I take it to beg the question. It also sets up a false dilemma: materialism or "God help us: we've let loose globlins, fairies, ghosts, demons, angels, demigods, and all manner of spooks into the universe such that science will be destroyed and we all will go hurling at full speed back to the Dark Ages."

Is that "quote mining"? No. I take this claim to illustrate an a priori commitment to materialism. Then I attack that commitment. [end quote]

Then don't take my class. I check footnotes, and that would be an automatic disqualifier in a paper.

Regardless whether one calls it "quote mining" or something else, it's academically dishonest. Lewontin was not arguing that science is religion, or should be accepted religiously. He was explaining why methodological naturalism is important as an experimental philosophy. We can't dismiss all science as "subject to change without notice," and expect any rational results. God may force your airplane to fall from the sky, but that's not to suggest that all aircraft flight should be suspect because of such a belief.

Lewontin actually was discussing methodology in science, not philosophy: "With great perception, Sagan sees that there is an impediment to the popular credibility of scientific claims about the world, an impediment that is almost invisible to most scientists. Many of the most fundamental claims of science are against common sense and seem absurd on their face. Do physicists really expect me to accept without serious qualms that the pungent cheese that I had for lunch is really made up of tiny, tasteless, odorless, colorless packets of energy with nothing but empty space between them? Astronomers tell us without apparent embarrassment that they can see stellar events that occurred millions of years ago, whereas we all know that we see things as they happen. When, at the time of the moon landing, a woman in rural Texas was interviewed about the event, she very sensibly refused to believe that the television pictures she had seen had come all the way from the moon, on the grounds that with her antenna she couldn't even get Dallas. What seems absurd depends on one's prejudice. Carl Sagan accepts, as I do, the duality of light, which is at the same time wave and particle, but he thinks that the consubstantiality of Father, Son, and Holy Ghost puts the mystery of the Holy Trinity "in deep trouble." Two's company, but three's a crowd.

Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything. To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen." [end quote]

More, Lewontin was discussing astronomy, not evolution.

At what point should we let facts have sway in an argument? Methodological naturalism, which says we accept the evidence we get from experiments, seems a whole lot more rational, and Christian, to me, than the philosophy that says we reject the data God's creation shows, because we want a laugh line at Lewontin's expense. The alternative is to say we cannot do astronomy; to say we cannot go to the Moon because, philosophically, we might be wrong about its existence; to say we should discontinue the search for a cure for cancer (or any other disease) because such a search frustrates God's obvious will (if God didn't mean Aunt Lil to get cancer, why did He cause it?). Accepting Lewontin's view on methodological naturalism is a better thing, theologically, than rejecting it.

Note also that Lewontin would not say that studying the actions of intelligent agents are disallowed in science. But questions of whether such an agent is supernatural is outside the range of study.

Tell me again what theistic science looks like? Phil Johnson has been pushing this angle for at least a decade but nothing has come out so far. Is it any different from what we do now in science? (Behe doesn't think so). Perhaps it would be something like a retread of Natural Theology, a discipline that successfully put itself out of business a couple centuries ago...

"Perhaps it would be something like a retread of Natural Theology, a discipline that successfully put itself out of business a couple centuries ago... "

Now there's an ignorant statement. Natural Theology has been on the rebound for several decades--and never was demolished by Hume and Kant as is often claimed. See "In Defense of Natural Theology," edited by James Sinnott and myself, "Reasonable Faith" by Willian Lane Craig, "Scaling the Secular City" by J.P. Moreland, the corpus of Richard Swinburne's work, and much more.

ID contributes to aspects of natural theology, but is cast more as a challenge to materialism in science; so, it is more of a new philosophy of science than part of natural theology per se.

Now there's an ignorant statement. Natural Theology has been on the rebound for several decades--and never was demolished by Hume and Kant as is often claimed.

Oh, I agree that one can't 'kill' Natural Theology but whether it is a terribly insightful means of describing the physical world in any useful detail is another matter. It never was terribly good at establishing convincing, positive & predictive connections in the direction *from* the supernatural/religious *to* the natural worlds. Science is the dog, Natural Theology is the tail and the dog wags the tail, not the other way around.

"James Sennett" not "Sinnott", yes?

I ask again: What does a useful theistic science look like? How would it differ procedurally or functionally from what science looks like today? Can it play by different rules with any success? That is the point Lewontin is making.

ID contributes to aspects of natural theology, but is cast more as a challenge to materialism in science; so, it is more of a new philosophy of science than part of natural theology per se.

Then it is perhaps the most bass ackwards strategy I've heard. ID cannot rule out or challenge 'materialism' in science. Science is methodologically materialistic: While it never brings in the supernatural it can also never rule out the supernatural. The supernatural would be binned in the category: "possible new interaction, cause not determined". As a proposal about the natural world, ID can at best say that some other forces or interactions are at work in nature. Science would attempt to characterize the interactions and determine some order behind phenomena.

Proponents may wish that ID could 'combat materialism' but that is a metaphysical/political add-on, a category error that has little to do with the actual practice or scope of science. The issue for the religious proponents of ID is not materialism in science, it's Materialism in culture. Those are far from the same thing and have far different implications in their respective scopes.

... I agree that one can't 'kill' Natural Theology but whether it is a terribly insightful means of describing the physical world in any useful detail is another matter. It never was terribly good at establishing convincing, positive & predictive connections in the direction *from* the supernatural/religious *to* the natural worlds.

I think this remark conflates Natural Theology with Theistic Science. NT isn't essentially a predictive enterprise; it takes data from everyday observation and, in some instances, from the sciences, and it attempts to draw inferences from those data.

Whatever Theistic Science is supposed to be -- and I think this is not terribly clear and that different people probably mean different things by the phrase -- it has to be more than that.

The claim that science would perforce come to a grinding halt if one allowed "a divine foot in the door" -- admitted miracles, to use Lewontin's phrase -- does not seem to be the outcome of any conspicuous line of argument. It is certainly difficult to maintain historically.

BTW, as far as I can see Doug's use of the Lewontin quotation is entirely legitimate. I understand that Ed doesn't like Doug's theology. But that wasn't the point at issue. Ed writes:

Regardless whether one calls it "quote mining" or something else, it's academically dishonest. Lewontin was not arguing that science is religion, or should be accepted religiously.

Did Doug claim this somewhere? If so, I missed it (again). If he didn't, what's the deal? Perhaps Ed is upset because he's seen others making this claim. But I submit to Ed that it's not reasonable to assimilate Doug's use of the Lewontin quotation to the use that someone else has made of it.

I'll move back to the point on hand: The problem of admitting 'miracles' in scientific explanations of phenomena. That is outside the scope of science (How does one define a 'miracle' in scientific terms?). At best, one can say something falls into the "Don't know what went on" category. Lack of knowledge or certainty has never prevented scientists from continuing efforts trying to expand our understanding. But calling something a miracle, as if that is the actual explanation and the proximate cause bypasses the operational methods by which science works. If one wishes to do that, fine. But don't pretend that it is science or that it is something that benefits the process.

From a historical perspective there were instances where some scientists once accepted miracles as viable explanations but we also have many examples where things formerly thought to be miraculous had 'natural' proximate explanations.

As for ID or Theistic science (pace Phil Johnson's wishes): The problem is not 'materialism' in science, it's one of positive formulation and productivity.

As for ID or Theistic science (pace Phil Johnson's wishes): The problem is not 'materialism' in science, it's one of positive formulation and productivity.

It's a matter of how productivity is defined. Recent minimal genome research projects are favorable to ID interpretations as are the non-productive results of some OOL projects. It is not the views of researchers that count. It is the data produced.

7. Do statistics show that a gene shared by different species most likely came from a common ancestor in the past?

8. Does the rate of gene mutation give an approximate time in the past for the existence of the common ancestor?

9. Take a random pool of 10 genes common to two species. Do you get the approximate same result for the age of the common ancestor when applying mutation rates for the entire pool of genes.

10. Take an entirely independent set of genes common to both species and compare for the common ancestor. Does the date match closely with 9 above.

11. Do the same test with "junk DNA.

12. Compare results for different species. Are the common ancestor dates consistent? For example is the common ancestor to mice and rats more recent than the common ancestor of mice and horses. Is the common ancestor of sea sponges and mice even more distant? Does this timetable hold true across all species?

The answer to all these questions is, "Yes."

The conclusion to be drawn is that all living things arose from a small group of common ancestors tha tpredate Wells' Cambrian explosion or anything else he'd like to talk about.

If intelligent Design was even partly true there would be some instances where the genetic mutations woudl be off and you would get inconsistent results in your nested phylogeny.

IF ID was true, you wouldn't be able to use DNA matches as evidence in court.

So there is direct evidence that speciation has occurred, that all creatures share a smallpool of common ancestores and more clsoely related creatures have more recent common ancestors.

William Bradford said: "Recent minimal genome research projects are favorable to ID interpretations as are the non-productive results of some OOL projects."

Since I'm looking at gene-finding right now, this is something I'd be very interested in. Can you please provide the details of these projects, and how they were favorable to ID? By "details of the projects", note that I mean enough information about them that I would be able to locate the project and examine their data directly.

Can you please provide the details of these projects, and how they were favorable to ID? By "details of the projects", note that I mean enough information about them that I would be able to locate the project and examine their data directly.

http://www.pnas.org/cgi/content/full/103/2/425

There are other references available. I suspect you are familiar with them. These papers are subject to interpretation from differing viewpoints. While differing views as to what would constitute minimal genomic function as well as minimal gene number exist, there is good reason to believe there is such a threshhold. If there is, what causal factors would produce such a genome?

william bradford wrote: "It's a matter of how productivity is defined."

How about providing information about the relationships between extant organisms and of those that existed in the past. What does ID tell us about similarity in DNA and protein sequences? What is behind the nested hierarchy of similarities observed in the history of life and why do the patterns tend to track across time, morphology, behavior, genetics and biochemistry? How does ID propose to connect the dots in terms of determinable causal factors? Or under any terms? As long as ID continues to define itself as a negative argument and 'designer of the gaps' it goes nowhere.

One could define productivity pretty loosely in the case of ID and still not find much. Wells had an idea about centrioles acting like turbines because they superficially resembled human-designed turbines. It was never clear how one associated the idea with a productive use of ID but that particular "prediction" seems to have dropped off the radar of late. William mentions references about minimal genomes being interpretable in the ID context. Yes, but what couldn't be interpreted in a ID context? It's always going to be like the Russian matrioshka nested dolls in which the discovery of a potential intermediate between species is advertised by IDers as creating *two* new unexplained gaps. What distinguishes ID from negative arguments? Is that the best it can do? Abiogenesis is a contested area that biologists are perfectly capable of debating without noting ID. The default explanation is: "Don't know".

As for what ID means in the history of life: Wells doesn't believe in common descent, Behe supports it, Denton says design was present in the Big Bang and merely needed to unfold through evolution, a fair number of IDers still think the Earth might only be a few thousand years old, and Phil Johnson won't let himself be pinned down to any strong opinion. What does ID *actually* represent? Back in the "my denver post review of two new books" article on this blog, I proposed straightforward criteria for choosing experimentally tractable systems for evaluating ideas like Behe's "irreducible complexity". The selection of model systems in biology can be tricky but any competent, motivated, life scientist should be able to pick out few. *IF* one wished to do actual biological research on ID that had some hope of realistically having any impact one way or the other, one might start there.

How about providing information about the relationships between extant organisms and of those that existed in the past. What does ID tell us about similarity in DNA and protein sequences?

Our knowledge of genomes indicates that the selective value of genes is dependent on the functional utility of the proteins. This leads to the question of not only what process would generate nucleic acids in a precellular world but what organic chemical reactions would accord the sequential arrangement required for coding function. Off to vote. I'll look at the rest later.

What is behind the nested hierarchy of similarities observed in the history of life and why do the patterns tend to track across time, morphology, behavior, genetics and biochemistry? How does ID propose to connect the dots in terms of determinable causal factors? Or under any terms? As long as ID continues to define itself as a negative argument and 'designer of the gaps' it goes nowhere.

ID proposes that at some point in natural history intelligence was a causal factor in determining the origin or subsequent development of life. You mentioned specific individuals who can speak for themselves. My own view is that intelligence can be inferred at point of origin. There are reasons. The causality you allude to, in connecting the dots, breaks down in a precellular world. In fact we are unable to assert, based on experimental data, that there could be a precursor cellular world. OOL models rely on a great deal of extrapolation and very dubious assumptions. Chief among them is the belief that the sequential order, characteristic of functional genomes, owes itself to a stochastic chemical process involving selection or a causal outcome made inevitable through a series of chemical reactions.

The gap accusation presumes an outcome not empirically demonstrated. There is also evidence that the seeds of destruction are sown into OOL models in the form of an inevitable and naturally occuring process that could corrupt encoding information in nucleic acids faster than it could be generated. The is prevented from occuring in cells only because mechanisms already exist preventing or repairing DNA damage and copying errors. This in turn suggests that cells lacking such mechanisms are not viable. Assertions to the contrary notwithstanding, ID does offer possible testable predictions.

Tim, what's the point of claiming anything about Lewontin's quote, by a creationist of any stripe? It's quote mining by any rational definition. Whatever Lewontin may have meant, he did not say what Groothuis and others claim he said, in context. He was not arguing for naturalism as philosophy, and it's misleading to claim he was.

If you think there is some other argument being made by creationists there, please define it. It's not apparent to me or anyone else familiar with science.

William Bradford writes: "The gap accusation presumes an outcome not empirically demonstrated."

Yes, like evidence that a designer was active and directly involved in the origin of life at the proposed time...

Does invoking design truly fill the gap in this case? As Freud said, "sometimes a cigar is just a cigar". A gap is a gap. The gap accusation presumes no outcome except that people should continue to seek workable explanations that actually provide real details. That's science. The origin of life is a thorny problem for both prebiotic researchers and IDers. But who is working to investigate possible mechanisms?

Sure. But are they distinguishable from possible evolutionary mechanisms? Are they significant or trivial? Would they create unambiguous results? Bad hypotheses can also generate testable predictions (some even come out true part of the time).

Personally, if someone wants to invoke design at the start of life, I'm cool with that. At this point we do not know what happened. Developing evidence to demonstrate that proposal is the real issue and a big problem. Unfortunately, unlike known designers, the "biotic" designer didn't appear to leave a lot of alternate evidence of its physical presence on Earth 4 billion years ago. Known designers tend to affect more than one thing or leave more that a single trace behind in the environment. Of course, the evidence could have been lost with geological activity. Or maybe it seeded life from an interstellar probe. Too bad the potential designer didn't leave something like a monolith on the moon. Of course, citing these problems can't be used to rule out design, but it is curious, no? It makes me ponder just how inhuman-like the potential designer could be. That's the problem of not having positive evidence to tease apart the essential details.

William, I've appreciated this conversation. I have had many others like it over the years and although it's unlikely to be resolved in our lifetimes, it is always interesting to see how new people take on the perpetual question (Myself, I'm interested in seeing how current life relates together and so I tend to focus on only the past 2 billion years or so, the times after the [apparently] three kingdoms of life emerged). But time to beg off and mind my family. Adios amigo!

Well Douglas wrote: "I take this claim to illustrate an a priori commitment to materialism. Then I attack that commitment.

If by this Doug suggested Lewontin has a commitment to metaphysical naturalism, then the quote is not indicative of that. He should search for other passages.

If Doug uses the quote to demonstrate that Lewontin thinks science has an a priori commitment to understand things with materialistic mechanisms, then it is trivial comment. That is what science *does*. This doesn't mean that non-material causes (whatever they are), couldn't actually be at the root of some particular material phenomenon, only that it's not going to be conclusively identified as such by scientific means. It will always be binned as "don't know". Science cannot provide that sort of certainty -- But other methods might. From these sort of discussions centered on the implied need to include "non-material" explanations in science (fight materialism!), I worry that some would like to say that supernatural phenomena can be "scientifically proven" or wish to seek some seal of approval from "science". Don't bother, for surely philosophers have come up with other systems of "knowing" stuff.

I suspect we may be talking past each other...Tim asks: Would it kill the process of science to sometimes propose non-material explanations?I respond: Sometimes no; sometimes yes. But what's the point of trying to smuggle in supernatural explanations? Science can't distinguish them from other unknown causes. It's asking something of science that science simply doesn't contain.

Tim, it's been good conversation with you as well. I've appreciated your thoughtful ideas, comments and helpful corrections. Adios!

William Bradford writes: "The gap accusation presumes an outcome not empirically demonstrated."

Yes, like evidence that a designer was active and directly involved in the origin of life at the proposed time...

To allege that the gap is in favor of the outcome you opine for rather than the outcome I believe in, is an expression of faith. IOW, the gap may not be attributable to a lack of knowledge but rather the failure of a presumed event to take place. Unspecified and empirically unsupported OOL pathways can be insertions into a gap.

Bradford pompously wrote:"Our knowledge of genomes indicates that the selective value of genes is dependent on the functional utility of the proteins."

Really? How does that apply in the case of, say, ribosomal RNA genes, which don't encode proteins at all?

It looks to me as though you have very little knowledge of genomes, Bill.

"This leads to the question of not only what process would generate nucleic acids in a precellular world but what organic chemical reactions would accord the sequential arrangement required for coding function."

Ribozymes, like ribosomal RNA, don't code for something else.

"...There is also evidence that the seeds of destruction are sown into OOL models in the form of an inevitable and naturally occuring process that could corrupt encoding information in nucleic acids faster than it could be generated."

Like what evidence?

"The is prevented from occuring in cells only because mechanisms already exist preventing or repairing DNA damage and copying errors."

Yet thousands of RNA viruses have no such mechanisms, they don't appropriate their host's mechanisms, and they exist, evolve, and can kill us very effectively.

"This in turn suggests that cells lacking such mechanisms are not viable."

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About Me

Nothing on this blog represents the position of Denver Seminary. I am a Christian, philosopher, teacher, writer, and preacher, who is Professor of Philosophy at Denver Seminary. My most recent of my eleven books is Christian Apologetics: A Comprehensive Case for Biblical Faith (InterVarsity Press, 2011). I have published ten others, including Truth Decay and On Jesus. I direct the Christian Apologetics and Ethics MA program at Denver Seminary.